Lecospec

Laboratory of Ecological Spectroscopy (lecospec)

The purpose lecospec code is to take ground or image based reflectance spectra, build a classifier or regression, apply that model to an imaging spectrometer data cube (aka hyperspectral image).

  1. First, install dependencies

    source(“./Scripts/Utilites/install_dependencies.R”)

  2. Then load the package of lecospectR

    source(“./Functions/lecospectR.R”)

The functions in lecospectR are divided into sections, Some functions are found in lecospectR.R but all of which are loaded by sourcing /Functions/lecospectR.R.

/Functions/dataframe_operations.R  
/Functions/model_support.R 
/Functions/pfts.R  
/Functions/pipeline.R  
/Functions/raster_operations.R 
/Functions/spectral_operations.R
/Functions/site_specific_processing.R   
/Functions/training_utilities.R    
/Functions/type_conversion.R   
/Functions/utilities.R 
/Functions/validation.R
/Functions/visualization.R

How to run lecospec

  1. Our workflow assumes a list of species with associated levels of taxonomic information (eg. functional group membership) /Data/SpeciesTable_202230417.csv. This table is used for several steps, including aggregating validation to the same taxonomic level as training data.

  2. Build a spectral library from a range of field scans collected with Tungsten halogen illumination using a leaf clip or contact probe. These scripts delete bad scans and standardize the associated information into a single metadata format. Around 90 vegetation indices are also calculated and the narrow band reflectance is resampled and smoothed to 5 nm bands.

    /Scripts/TrainingDataCreation/Ground/2_DataMunging.R
    /Scripts/TrainingDataCreation/Ground/2B_DataMunging_missing_spectra.R
    /Scripts/TrainingDataCreation/Ground/3_Create_SpecLibPSR.R

The output of running these scripts is spectral library reflectance and the metadata.

/Output/C_001_SC3_Cleaned_SpectralLib.csv

  1. Collect spectra from pixels in images from UAV in quadrats and patches of plant functional types visible in ground reference or higher resolution RGB imagery. Calculate vegetation indices, smooth and resample spectra to 5 nm wide bands. Reflectance spectra are extracted from hand digitized patches of plant functional types provided as a shapefile to the first script (101_Crop_Training_PFT_vector). The same operation is performed in the second script (101_Crop_Training_Quads) for hand digitzed quadrats of validation ground cover data. Script 102_Parse_training_PFT_vector_spectra adds metadata to each pixel by plant patch.

    “/Scripts/TrainingDataCreation/Image/101_Crop_Training_PFT_vector.R” “/Scripts/TrainingDataCreation/Image/101_Crop_Training_Quads.R” “/Scripts/TrainingDataCreation/Image/102_Parse_training_PFT_vector_spectra.R”
    “/Scripts/TrainingDataCreation/Image/103_Clean_training_PFT_vector_spectra.R”

After running these scripts, the output is relectance for each pixel from the patches of plants digitized from images.

/Data/Ground_Validation/PFT_Image_spectra/PFT_Image_SpectralLib_Clean.csv

After cleaning scans, the reflectance data can be summarized and visualized in various ways. For example, running elements of the /Scripts/ExploratoryDataAnalysis/7_Visualizations_JGR_Bio_Tundra_Refl.R produce the the figure below, which shows the median and interquartile ranges of reflectance (75% black & 95% grey) with the sample size in number of scans distributed across a number of scans (ground measured) or pixels (airborne).

Study Area and Data locations

The centers of all UAV flights and points where ground scans were collected are shown in the map. Collecting these locations from the metadata and image centers for data collected as the Arctic boreal plant mapping use case for lecospectR using the /Scripts/ExploratoryDataAnalysis/7_Visualizations_Ground_and_UAS_Spectra_locations.R which produces the two .kml files plotted in the map below. The image below it shows one site (Bison Gulch near Denali National Park) with ground validation quadrat locations (squares) along 100 m long transect with a white calibration tarp on one end.

Model training and validation

  1. Set all the input, output and needed associated files for building models and predicting images

    /Scripts/validation_def.R

Variable set in this script include: test_paths, which are rasters only with the pixels by quadrat by site shape_paths, which are the vectors of the edges of each quadrat by site validation_paths, which are tabular data of ocular estimated cover of plants by a human based on ground photos lists of names of quadrat vectors by site (eg. bison_gulch_names <- c(“Bisongulch0”,“Bisongulch60”,“Bisongulch70”,“Bisongulch10”,“Bisongulch80”,“Bisongulch20”,“Bisongulch50”,“Bisongulch30”,“Bisongulch40”))

In this script, The test_paths are set to the output of /Scripts/TrainingDataCreation/101_Crop_Training_PFT_vector, which are a set of images with 326 bands from 400-1000nm covering only the square quadrats 1m x 1m that were hand digitized in different study areas. Model paths are set for different types to be evaluated. The vector layers of each hand digitized quadrats are set in tihe shape_paths. The names of each quadrat are listed manually to standardize across all since each vector layer of quadrats follow different order and have slightly different names. The validation_path are the ground cover estimates by quadrat derived from ground photos by a single expert observer.

  1. Proprocessing spectral libraries Using the notebook below, a variety of proprocessing is applied to the ground and image based spectral libraries created in earlier steps. Preprocessing options/steps include, resampling and smoothing spectra to 5nm wide bands, filtering out sites (which would have to then be excluded from Scripts/validation_defs.R), clipping outliers, building a sensor correction model between ground and image spectra libraries, a few different types of rescaling (after smoothing) and finally creating a training and test split for each dataset. These train and test splits are written to disk in /Data/gs in x_train or x_test (independent variables) and y_train and y_test (dependent variables)

/Scripts/TrainingDataCreation/speclib_processing.ipynb

  1. Builds and visualizes model accuracy

Two scripts build, validate and visualize accuracy of two different kinds of models; random forests implemented in the ranger package and partial least squares regression linear discriminant analysis (PLS-LDA).

/Scripts/grid_search_rf.R   
/Scripts/grid_search_PLS.R

Here is an example confusion matrix from a model showing misclassification between plant funcational types.

  1. After exploring models based on different input data, Pick and model and explore results with lecospectR::validate_model.R , whicih calls the input data, models and settings from validate_def.R

    /mle/“MODEL UUID HERE”

  2. Generate predidctions for plant functional type occurence for whole datacubes by running the parallelized estimate_landcover function from lecospectR. Set the number of tiles carefully based on RAM and image size. To run the function lecospectR::estimate_landcover, check the settings in the /config.json. The settings include

    automatic_tiling: false
    max_size: 200
    x_tiles: 2 # Set to make about 10% of RAM size on machine
    y_tiles: 2
    tile_path: “./tiles/” #Intermediate products go here, like /temp. Will need to be cleaned out every so often
    model_path: “./mle/”INSERT MOD NAME”.rda” #Models built in /modelbuilding.ipynb can be pasted here
    clusterCores: (NUM CORES ON MACHINE - 1) #Speeds up the processing on larger images to have more cores but tradeoff between handling tiles and creating tiles exists
    parallelize_by_tiles: false key_path: “./fg2key.json”
    external_bands: “./bands.csv” #Bands used to rename spectral objects consistently along the way output_format: “grd”
    aggregation: 1 #Depends on levels within data and only relevant for taxonomic-like structured response categories

Once the /config.json is set to match what is needed, the following script shows specifying a single large image and smaller images used in estimate_landcover.

/Scripts/run.R

  1. Visualize maps of full image output showing plant functional types

    /Scripts/visualizeRasters.R

Example predicted plant functional type map from one site (Bison Gulch near Denali National Park)